SMTL ID : 2cdp.1 (3 other biounits)

Structure of a CBM6 in complex with neoagarohexaose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

1 x GAL- AAL- GAL- AAL- GAL- AAL: 3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose

GAL-AAL-GAL-AAL-GAL-AAL.1: 6 residues within 4Å: Chain A: N.61, Y.62, V.91, W.119, W.149, N.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.61, A:Y.62, A:N.152 Water bridges: A:Y.62, A:Y.62, A:V.63, A:N.147

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: E.30, E.32, T.58, D.154 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.30, A:E.32, A:E.32, A:T.58, H2O.2 CA.3: 5 residues within 4Å: Chain A: D.43, P.48, Y.62, N.64, D.67 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.43, A:P.48, A:Y.62, A:D.67, H2O.1

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: V.111, T.112, G.127, G.128 Ligands: CL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.127 Water bridges: A:V.111

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain A: T.110, V.111 Ligands: EDO.4 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: V.29, E.30, N.33 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: V.130, Y.131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Henshaw, J. et al., Family 6 Carbohydrate Binding Modules in Beta-Agarases Display Exquisite Selectivity for the Non- Reducing Termini of Agarose Chains. J.Biol.Chem. (2006)

Release Date

2006-02-08

Peptides

BETA-AGARASE 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

BETA-AGARASE 1

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